Molecular Engineering of the Peptoid Nanosheet Hydrophobic Core

Unique Crystal Structure of a Self-Assembled Dinuclear Cu Peptoid Reveals an Unusually Long Cu···Cu Distance

Studies on a series of molecular dicopper peptoid complexes showed that the Cu···Cu distances measured in X-ray single-crystal diffraction are typically in the range of 4.2-6.9 Å. Herein, we designed a new peptoid, L1, having 2,2'-bipyridine, propyl, and pyridyl side chains and discovered that although it forms a typical dicopper self-assembled structure (complex 1), the Cu···Cu distance is exceedingly long -8.043 Å. By analyzing its structure and surface properties in comparison to a control Cu-peptoid complex (2), in which the pyridyl side chain is modified by an ethanolic side chain, we suggest that the long Cu···Cu distance is contributed by the hydrophilic-hydrophobic interaction influenced by the pyridyl side chain and the steric hindrance of the propyl side chain. This result may motivate the use of dinuclear Cu peptoid complexes for wider applications, such as cooperative catalysis and luminescence.

Synthetically encoded complementary oligomers

Creating the next generation of advanced materials will require controlling molecular architecture to a degree typically achieved only in biopolymers. Sequence-defined polymers take inspiration from biology by using chain length and monomer sequence as handles for tuning structure and function. These sequence-defined polymers can assemble into discrete structures, such as molecular duplexes, via reversible interactions between functional groups. Selectivity can be attained by tuning the monomer sequence, thereby creating the need for chemical platforms that can produce sequence-defined polymers at scale. Developing sequence-defined polymers that are specific for their complementary sequence and achieve their desired binding strengths is critical for producing increasingly complex structures for new functional materials. In this Review Article, we discuss synthetic platforms that produce sequence-defined, duplex-forming oligomers of varying length, strength and association mode, and highlight several analytical techniques used to characterize their hybridization.

Two-Dimensional Supramolecular Polymerization of DNA Amphiphiles is Driven by Sequence-Dependent DNA-Chromophore Interactions

Two-dimensional (2D) assemblies of water-soluble block copolymers have been limited by a dearth of systematic studies that relate polymer structure to pathway mechanism and supramolecular morphology. Here, we employ sequence-defined triblock DNA amphiphiles for the supramolecular polymerization of free-standing DNA nanosheets in water. Our systematic modulation of amphiphile sequence shows the alkyl chain core forming a cell membrane-like structure and the distal π-stacking chromophore block folding back to interact with the hydrophilic DNA block on the nanosheet surface. This interaction is crucial to sheet formation, marked by a chiral "signature", and sensitive to DNA sequence, where nanosheets form with a mixed sequence, but not with a homogeneous poly(thymine) sequence. This work opens the possibility of forming well-ordered, bilayer-like assemblies using a single DNA amphiphile for applications in cell sensing, nucleic acid therapeutic delivery and enzyme arrays.

Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes

Peptoids (N-substituted glycines) are a group of highly controllable peptidomimetic polymers. Amphiphilic diblock peptoids have been engineered to assemble crystalline nanospheres, nanofibrils, nanosheets, and nanotubes with biochemical, biomedical, and bioengineering applications. The mechanical properties of peptoid nanoaggregates and their relationship to the emergent self-assembled morphologies have been relatively unexplored and are critical for the rational design of peptoid nanomaterials. In this work, we consider a family of amphiphilic diblock peptoids consisting of a prototypical tube-former (Nbrpm6Nc6, a NH₂-capped hydrophobic block of six N-((4-bromophenyl)methyl)glycine residues conjugated to a polar NH₃(CH₂)₅CO tail), a prototypical sheet-former (Nbrpe6Nc6, where the hydrophobic block comprises six N-((4-bromophenyl)ethyl)glycine residues), and an intermediate sequence that forms mixed structures ((NbrpeNbrpm)3Nc6). We combine all-atom molecular dynamics simulations and atomic force microscopy to determine the mechanical properties of the self-assembled 2D crystalline nanosheets and relate these properties to the observed self-assembled morphologies. We find good agreement between our computational predictions and experimental measurements of Young's modulus of crystalline nanosheets. A computational analysis of the bending modulus along the two axes of the planar crystalline nanosheets reveals bending to be more favorable along the axis in which the peptoids stack by interdigitation of the side chains compared to that in which they form columnar crystals with π-stacked side chains. We construct molecular models of nanotubes of the Nbrpm6Nc6 tube-forming peptoid and predict a stability optimum in good agreement with experimental measurements. A theoretical model of nanotube stability suggests that this optimum is a free energy minimum corresponding to a "Goldilocks" tube radius at which capillary wave fluctuations in the tube wall are minimized.

A mini-review on bio-inspired polymer self-assembly: single-component and interactive polymer systems

Biology demonstrates meticulous ways to control biomaterials self-assemble into ordered and disordered structures to carry out necessary bioprocesses. Empowering the synthetic polymers to self-assemble like biomaterials is a hallmark of polymer physics studies. Unlike protein engineering, polymer science demystifies self-assembly by purposely embedding particular functional groups into the backbone of the polymer while isolating others. The polymer field has now entered an era of advancing materials design by mimicking nature to a very large extend. For example, we can make sequence-specific polymers to study highly ordered mesostructures similar to studying proteins, and use charged polymers to study liquid-liquid phase separation as in membraneless organelles. This mini-review summarizes recent advances in studying self-assembly using bio-inspired strategies on single-component and multi-component systems. Sequence-defined techniques are used to make on-demand hybrid materials to isolate the effects of chirality and chemistry in synthetic block copolymer self-assembly. In the meantime, sequence patterning leads to more hierarchical assemblies comprised of only hydrophobic and hydrophilic comonomers. The second half of the review discusses complex coacervates formed as a result of the associative charge interactions of oppositely charged polyelectrolytes. The tunable phase behavior and viscoelasticity are unique in studying liquid macrophase separation because the slow polymer relaxation comes primarily from charge interactions. Studies of bio-inspired polymer self-assembly significantly impact how we optimize user-defined materials on a molecular level.

Tuning the Packing Density of Gold Nanoparticles in Peptoid Nanosheets Prepared at the Oil-Water Interface

Two-dimensional (2D) arrays of gold nanoparticles that can freely float in water are promising materials for solution-based plasmonic applications like sensing. To be effective sensors, it is critical to control the interparticle gap distance and thus the plasmonic properties of the 2D arrays. Here, we demonstrate excellent control over the interparticle gap distance in a family of freely floating gold nanoparticle-embedded peptoid nanosheets. Nanosheets are made via monolayer assembly and collapse at the oil-water interface, allowing for fine control over the solution nanoparticle concentration during assembly. We used surface pressure measurements to monitor the assembly of the peptoid, nanoparticle, and combined system at the oil-water interface to determine a workable range of nanosheet assembly conditions suitable for controlling the interparticle gap distances within the nanosheets. These measurements revealed that the extent of nanoparticle adsorption to the peptoid monolayer can be tuned by varying the bulk nanoparticle concentration, but the ability for the monolayer to collapse into nanosheets is compromised at high nanoparticle concentrations. Peptoid nanosheets were synthesized with varying bulk nanoparticle concentrations and analyzed using light microscopy and UV-visible spectroscopy. Based on the spectral shift of the localized surface plasmon resonance peaks for the nanoparticles in the nanosheets relative to those well dispersed in toluene, we estimate that we can access interparticle gap distances within the nanosheet interior between 2.9 ± 0.5 and 9 ± 2 nm. Our results suggest that the minimum interparticle distance achievable by this method is limited by the nanoparticle ligand length, and so has the potential to be further tuned by varying the ligand chemical structure. The ability to quantitatively control and monitor the assembly conditions by this method provide an opportunity to readily tune the optoelectronic properties of this new class of 2D nanomaterial, making it a promising platform for plasmonic-based sensing applications.

Advances in hybrid peptide-based self-assembly systems and their applications

Self-assembly of peptides demonstrates a great potential for designing highly ordered, finely tailored supramolecular arrangements enriched with high specificity, improved efficacy and biological activity. Along with natural peptides, hybrid peptide systems composed of natural and chemically diverse unnatural amino acids have been used in various fields, including drug delivery, wound healing, potent inhibition of diseases, and prevention of biomaterial related diseases to name a few. In this review, we provide a brief outline of various methods that have been utilized for obtaining fascinating structures that create an avenue to reproduce a range of functions resulting from these folds. An overview of different self-assembled structures as well as their applications will also be provided. We believe that this review is very relevant to the current scenario and will cover conformations of hybrid peptides and resulting self-assemblies from the late 20^th century through 2022. This review aims to be a comprehensive and reliable account of the hybrid peptide-based self-assembly owing to its enormous influence in understanding and mimicking biological processes.

Hierarchical assemblies of polypeptoids for rational design of advanced functional nanomaterials

Polypeptoids (poly-N-substituent glycines) are a class of highly tailorable peptidomimetic polymers. Polypeptoids have identical backbones as polypeptides (poly-C-substituent glycines), but sidechains of polypeptoids are appended to backbone nitrogen rather than α-carbon of polypeptides. As a result, peptoid backbone lacks of chirality and hydrogen bond donors. This unique structure gives polypeptoids a combined merit of both high stability as synthetic polymers and biocompatibility as biopolymers. In addition, peptoid sequences can be engineered precisely to assemble specific crystalline patterns such as spheres, fibers, ribbons, tubes, and sheets, which shows promising potentials of polypeptoids for different applications such as antimicrobials, catalysts, drug delivery, and templating inorganic materials. In this review, we summarize recent investigations into hierarchical self-assembly pathways and molecular structures of peptoid crystals that are of interest as templates for fabricating functional materials for potential biomedical, biochemical, and bioengineering applications. This review provides a summary of recent experimental and computational studies of polypeptoid assembly in solution and solid-liquid interfaces, current achievements in the field, and discusses future challenges and opportunities for the rational design of self-assembled polypeptoid nanomaterials.

Hierarchical Nanomaterials Assembled from Peptoids and Other Sequence-Defined Synthetic Polymers

In nature, the self-assembly of sequence-specific biopolymers into hierarchical structures plays an essential role in the construction of functional biomaterials. To develop synthetic materials that can mimic and surpass the function of these natural counterparts, various sequence-defined bio- and biomimetic polymers have been developed and exploited as building blocks for hierarchical self-assembly. This review summarizes the recent advances in the molecular self-assembly of hierarchical nanomaterials based on peptoids (or poly-N-substituted glycines) and other sequence-defined synthetic polymers. Modern techniques to monitor the assembly mechanisms and characterize the physicochemical properties of these self-assembly systems are highlighted. In addition, discussions about their potential applications in biomedical sciences and renewable energy are also included. This review aims to highlight essential features of sequence-defined synthetic polymers (e.g., high stability and protein-like high-information content) and how these unique features enable the construction of robust biomimetic functional materials with high programmability and predictability, with an emphasis on peptoids and their self-assembled nanomaterials.

Early-Stage Aggregation and Crystalline Interactions of Peptoid Nanomembranes

Fully synthetic peptoid membranes are known to mimic important features of biological membranes, with several advantages over other biomimetic membranes. A fundamental understanding of how the individual peptoid amphiphiles assemble in solution to form the bilayer membrane is key to unlocking their versatility for application in a broad range of processes. In this study, in situ X-ray scattering and molecular dynamics simulations are used to understand the early stages of assembly of three different peptoids that exhibit distinctly different crystallization kinetics. The in situ measurements reveal that the peptoids aggregate first into a nascent phase that is less crystalline than the assembled peptoid membrane. Anisotropic aromatic interactions are determined to be the dominant driving force in the early stages of membrane formation. These results provide key insights into how the peptoid assembly may be manipulated during the early stages of assembly and nucleation and growth.

Submonomer synthesis of peptoids containing trans-inducing N-imino- and N-alkylamino-glycines

The use of hydrazones as a new type of submonomer in peptoid synthesis is described, giving access to peptoid monomers that are structure-inducing. A wide range of hydrazones were found to readily react with α-bromoamides in routine solid phase peptoid submonomer synthesis. Conditions to promote a one-pot cleavage of the peptoid from the resin and reduction to the corresponding N-alkylamino side chains were also identified, and both the N-imino- and N-alkylamino glycine residues were found to favor the trans-amide bond geometry by NMR, X-ray crystallography, and computational analyses.

Smart supramolecular nanofibers and nanoribbons from uniform amphiphilic azobenzene oligomers

A series of self-assembled 1D nanostructures, including straight and helix nanofibers, nanoribbons, and nanobelts, were fabricated from uniform amphiphilic azobenzene oligomers with tunable molecular weight and side chain functionality, promoted by multiple and cooperative supramolecular interactions. Additionally, the morphological transformation of the nanofibers was achieved during the photoisomerization process.

Nanoparticle-Mediated Assembly of Peptoid Nanosheets Functionalized with Solid-Binding Proteins: Designing Heterostructures for Hierarchy

The fabrication of ordered architectures that intimately integrate polymer, protein, and inorganic components remains difficult. Two promising building blocks to tackle this challenge are peptoids, peptide mimics capable of self-assembly into well-defined structures, and solid-binding peptides, which offer a biological path to controlled inorganic assembly. Here, we report on the synthesis of 3.3-nm-thick thiol-reactive peptoid nanosheets from equimolar mixtures of unmodified and maleimide-derivatized versions of the Nbpe₆Nce₆ oligomer, optimize the location of engineered cysteine residues in silica-binding derivatives of superfolder green fluorescent protein for maleimide conjugation, and react the two components to form protein-peptoid hybrids exhibiting partial or uniform protein coverage on both of their sides. Using 10 nm silica nanoparticles, we trigger the stacking of these 2D structures into a multilayered material composed of alternating peptoid, protein, and organic layers. This simple and modular approach to hierarchical hybrid synthesis should prove useful in bioimaging and photocatalysis applications.

Controlled ring-opening polymerization of N-(3-tert-butoxy-3-oxopropyl) glycine derived N-carboxyanhydrides towards well-defined peptoid-based polyacids

Polypeptoids bearing carboxylic acid groups on the N-substituent are useful building blocks for the construction of peptidomimetic supramolecular assemblies with stimuli-responsive properties.

The Diverse World of Foldamers: Endless Possibilities of Self-Assembly

Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.

Lipid-anchor display on peptoid nanosheets via co-assembly for multivalent pathogen recognition

Biological systems have evolved sophisticated molecular assemblies capable of exquisite molecular recognition across length scales ranging from angstroms to microns. For instance, the self-organization of glycolipids and glycoproteins on cell membranes allows for molecular recognition of a diversity of ligands ranging from small molecules and proteins to viruses and whole cells. A distinguishing feature of these 2D surfaces is they achieve exceptional binding selectivity and avidity by exploiting multivalent binding interactions. Here we develop a 2D ligand display platform based on peptoid nanosheets that mimics the structure and function of the cell membrane. A variety of small-molecule lipid-conjugates were co-assembled with the peptoid chains to create a diversity of functionalized nanosheet bilayers with varying display densities. The functional heads of the lipids were shown to be surface-exposed, and the carbon tails immobilized into the hydrophobic interior. We demonstrate that saccharide-functionalized nanosheets (e.g., made from globotriaosylsphingosine or 1,2-dipalmitoyl-sn-glycero-3-phospho((ethyl-1',2',3'-triazole)triethyleneglycolmannose)) can have very diverse binding properties, exhibiting specific binding to multivalent proteins as well as to intact bacterial cells. Analysis of sugar display densities revealed that Shiga toxin 1 subunit B (a pentameric protein) and FimH-expressing Escherichia coli (E. coli) bind through the cooperative binding behavior of multiple carbohydrates. The ability to readily incorporate and display a wide variety of lipidated cargo on the surface of peptoid nanosheets makes this a convenient route to soluble, cell-surface mimetic materials. These materials hold great promise for drug screening, biosensing, bioremediation, and as a means to combat pathogens by direct physical binding through a well-defined, multivalent 2D material.

Atomic-level engineering and imaging of polypeptoid crystal lattices

A fundamental challenge in materials science is to understand the atomic-level structures of nanoarchitectures assembled from synthetic polymers. Here, we report a family of sequence-defined polypeptoids that form free-floating crystalline 2-dimensional nanosheets, in which not only individual polymer chains and their relative orientations, but also atoms in nanosheets were directly observed by cryogenic transmission electron microscopy. These atomic details are inaccessible by conventional scattering techniques. Using the feedback between sequence-controlled synthesis and atomic imaging, we observed how the nanosheet structure responds to chemical modifications at the atomic-length scale. These atomic-level insights open the door to the design of bioinspired nanomaterials with more precisely controlled structures and properties.

Rational design of supramolecular nanomaterials fundamentally depends upon an atomic-level understanding of their structure and how it responds to chemical modifications. Here we studied a series of crystalline diblock copolypeptoids by a combination of sequence-controlled synthesis, cryogenic transmission electron microscopy, and molecular dynamics simulation. This family of amphiphilic polypeptoids formed free-floating 2-dimensional monolayer nanosheets, in which individual polymer chains and their relative orientations could be directly observed. Furthermore, bromine atom side-chain substituents in nanosheets were directly visualized by cryogenic transmission electron microscopy, revealing atomic details in position space inaccessible by conventional scattering techniques. While the polypeptoid backbone conformation was conserved across the set of molecules, the nanosheets exhibited different lattice packing geometries dependent on the aromatic side chain para substitutions. Peptoids are inherently achiral, yet we showed that sequences containing an asymmetric aromatic substitution pattern pack with alternating rows adopting opposite backbone chiralities. These atomic-level insights into peptoid nanosheet crystal structure provide guidance for the future design of bioinspired nanomaterials with more precisely controlled structures and properties.

Peptoids as tools and sensors

A review of molecular tools and sensors assembled on N-substituted glycine, or α-peptoid, oligomers between 2013 and November 2018 with the following sections: (a) Peptoids as crystal growth modifiers, (b) Peptoids as catalysts, (c) Ion and molecule sequestration and transport, (d) Peptoid sensors, (e) Macromolecule recognition, (f) Cellular transporters, (g) Medical imaging, (h) Future direction and (i) Summary and outlook. Peptoids are a promising class of peptide mimic making them an excellent platform for functional molecule preparation. Attributes of peptoid oligomers include: (a) the ease of precise sequence definition and mono-dispersity; (b) access to a vast chemical space within simple and repeating chemical preparative steps and (c) thermal, chemical and biological stability all lending support for their application in a number of areas, with some that have been realised to date. The peptoid tool and sensor examples selected have realised practical utility. They serve to illustrate the rapidity of new insight that can generate in many disparate areas of science and technology, enabling the quick assembly of design criteria for efficient peptoid molecular tools and sensors.

Crystallization and lamellar nanosheet formation of an aromatic dipeptoid

An aromatic peptoid analogue of the diphenylalanine dipeptide self-assembles in aqueous solution and the first crystal structure was obtained for this class of compound.

Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions

The conformations adopted by the molecular constituents of a supramolecular assembly influence its large-scale order. At the same time, the interactions made in assemblies by molecules can influence their conformations. Here we study this interplay in extended flat nanosheets made from nonnatural sequence-specific peptoid polymers. Nanosheets exist because individual polymers can be linear and untwisted, by virtue of polymer backbone elements adopting alternating rotational states whose twists oppose and cancel. Using molecular dynamics and quantum mechanical simulations, together with experimental data, we explore the design space of flat nanostructures built from peptoids. We show that several sets of peptoid backbone conformations are consistent with their being linear, but the specific combination observed in experiment is determined by a combination of backbone energetics and the interactions made within the nanosheet. Our results provide a molecular model of the peptoid nanosheet consistent with all available experimental data and show that its structure results from a combination of intra- and intermolecular interactions.

Assembly and Self-Assembly of Nanomembrane Materials-From 2D to 3D

Nanoscience and nanotechnology offer great opportunities and challenges in both fundamental research and practical applications, which require precise control of building blocks with micro/nanoscale resolution in both individual and mass-production ways. The recent and intensive nanotechnology development gives birth to a new focus on nanomembrane materials, which are defined as structures with thickness limited to about one to several hundred nanometers and with much larger (typically at least two orders of magnitude larger, or even macroscopic scale) lateral dimensions. Nanomembranes can be readily processed in an accurate manner and integrated into functional devices and systems. In this Review, a nanotechnology perspective of nanomembranes is provided, with examples of science and applications in semiconductor, metal, insulator, polymer, and composite materials. Assisted assembly of nanomembranes leads to wrinkled/buckled geometries for flexible electronics and stacked structures for applications in photonics and thermoelectrics. Inspired by kirigami/origami, self-assembled 3D structures are constructed via strain engineering. Many advanced materials have begun to be explored in the format of nanomembranes and extend to biomimetic and 2D materials for various applications. Nanomembranes, as a new type of nanomaterials, allow nanotechnology in a controllable and precise way for practical applications and promise great potential for future nanorelated products.

Structure-Rheology Relationship in Nanosheet-Forming Peptoid Monolayers

Peptoid nanosheets are novel protein-mimetic materials that form from the supramolecular assembly of sequence-defined peptoid polymers. The component polymer chains organize themselves via a unique mechanism at the air-water interface, in which the collapse of a compressed peptoid monolayer results in free-floating, bilayer nanosheets. To impart functionality into these bilayer materials, structural engineering of the nanosheet-forming peptoid strand is necessary. We previously synthesized a series of peptoid analogues with modifications to the hydrophobic core in order to probe the nanosheet tolerance to different packing interactions. Although many substitutions were well-tolerated, routine surface pressure measurements and monolayer collapse isotherms were insufficient to explain which molecular processes contributed to the ability or inability of these peptoid analogues to form nanosheets. Here, we show that surface dilational rheology measurements of assembled peptoid monolayers at the air-water interface provide great insight into their nanosheet-forming ability. We find that a key property required for nanosheet formation is the ability to assemble into a solidlike monolayer in which the residence time of the peptoid within the monolayer is very long and does not exchange rapidly with the subphase. These collapse-competent monolayers typically have a characteristic time of diffusion-exchange values, τ_D, of >5000 s. Thus, rheological measurements provide an efficient method for assessing the nanosheet-forming ability of peptoid analogues. Results from these studies can be used to guide the rational design of peptoids for assembly into functional nanosheets.